Resolution Pyramids
Stitch and render massive full-resolution images on a low-RAM computer
Note: Available for Huygens Professional only
Microscopy images continue to grow in size, challenging - and often exceeding - the RAM capacity of computers. To overcome this limitation, downsampling or cropping is often applied, inevitably resulting in a loss of image data and/or quality.
Huygens' Resolution Pyramid file format, available in Professional offers a solution. It enables the stitching and visualization of massive datasets (gigabytes - terabytes) without compromising image quality. Even on low-end computers, large images can be opened, viewed, and stitched with ease.
Huygens Resolution Pyramid files can also be exported to Bio-Formats- and BigDataViewer-compatible images, while preserving the full metadata and pixel information preserved (see below for details).
How does it work?
Even high-resolution monitors cannot display every pixel of a large image. Resolution Pyramid files therefore display a downsampled version until you zoom in, loading higher-resolution data only for the area in view. This keeps RAM usage low.
The same principle applies to stitching: only a single tile and its neighbours need to be loaded at a time to stitch the entire dataset into a Resolution Pyramid mosaic.
No data is lost. Resolution Pyramid files preserve the original image, downsampled versions, metadata, and statistics, all of which remain available for extraction whenever needed.
Always view the optimal resolution!
bypasses RAM limits with uncompromising detail
Hover over images to enlarge
RAM limit requires down-sampling, degrading image quality
Hover over images to enlarge
Left: Using Huygens’ new Resolution Pyramid HDF51 file format .pyr.h5, you can save and view extreme large datasets with the precision they deserve. The dark gray triangle icons in the left Twin Slicer images indicate that they are part of a Resolution Pyramid file, and the highlighted layer shows what resolution level is displayed.
Right: Classical approach: If no pyramid file format is used, images may need down-sampling to decrease file size for viewing and further image processing, thus compromising image quality.
Exclusive to Huygens Professional from version 25.10
Contact us for options to upgrade your Huygens Essential to Professional!
Pyramids can be generated from all image formats2
Stitch extremely large datasets at full resolution
View images far exceeding a device's RAM
Save as Huygens’ .pyr.h5 format
Save as Bioformats and BDV compatible Resolution Pyramid format. (since Huygens 26.04)
Extract or Crop full and downsampled versions from the .pyr.h5 format
Compatible with Huygens Stitcher, Slicers, SFP and MIP Renderers, and Cropper.
Notice: Any image (or a few tiles) that can be opened in Huygens Professional can be saved to a Resolution Pyramid format. For larger files, see footnote2.
Diagrams showcasing three scenarios with an oversized file
Huygens’ Resolution Pyramids work with the HDF5 based file format, which is saved on the computers storage and contains the same image at different resolutions. The bottom tier contains the full resolution image, but cropped into smaller chunks. Tiers above this contain down-sampled versions made of fewer and larger chunks. These down-sampled versions contain less true detail, but are smaller in size and appear just as detailed on a monitor (at the zoom levels they are displayed at).
No Resolution Pyramid: The image cannot be opened in Huygens if the device does not have sufficient RAM to fit it, and Huygens Resolution Pyramid option is not used.
Resolution Pyramid: Images can be stiched and/or converted into a Resolution Pyramid file. Huygens loads higher resolution information only for the area that is visualized, thus minimizing RAM usages. Creates smaller file sizes than complete Pyramids, yet leads to detail loss when using a lower resolution.
Working with Huygens Resolution Pyramids
How to create Resolution Pyramid files in Professional:
1) navigate to File > Generate Resolution Pyramid, choose an image and save location for the conversion process (this conversion can use RAM and virtual RAM and allows conversion of files larger than the available RAM; see 2nd footnote).
2) open any image in Huygens that fits in RAM, and convert it by selecting from the Tools menu in the task bar the pyramid file icon.
3) in batch-mode use the Workflow Processor with "File conversion" as a workflow Preset. Workflow templates can also be used via the command line interface of Core.
4) use the Stitcher to save the final output as a Resolution Pyramid to storage.
There is the option to calculate a histogram from the original high resolution image. This option can be disabled to save time in the conversion process. This will result in a file that does include a histogram. If needed, you can always calculated a histogram after conversion.
How to extract a Resolution level
To extract a single image from at a specific resolution level, navigate to the main menu, where your Resolution Pyramid is loaded. From here you can right-click and use Extract Layer. This generates an image in Huygens that you can use for operations, or save as a standalone image e.g. as HDF5.
How to crop a volume, channel, time frame and resolution level
Resolution Pyramid files can be opened with the " Crop image" tool (Tools menu) to extract specific information. The size of the selected information for cropping is conveniently presented in the Crop option. Cropping a smaller part of the image data can facilitate its rendering and analysis on computers with limited RAM.
Compatability with other software
The Huygens Resolution Pyramid .pyr.h5 file itself is exclusive to Huygens software. However, it can be converted in Huygens Professional to a Bioformats/BigDataViewer compatible version that includes:
a. the regular Huygens Resolution Pyramid .pyr.h5 file
b. and two accompanying files with filename_bdv.h5 and filename_bdv.xml, which are read by Bio-Formats and BigDataViewer.
Footnotes/References
- Huygens HDF5 (Pyramid) file format is based on the Hierarchical Data Format version 5 (HDF5), which is an open source file format that supports large, complex, heterogeneous data. Huygens HDF5 stores extensive metadata information of all the supported microscope types, including STED, Light Sheet and Array Detector based systems. This information can be read by free HDF5 readers. Saving Huygens Resolution Pyramid files to a Bioformats and BigDataviewer compatible version in Huygens Professional allows opening of the full image and its sub-resolution versions. For more information, see http://www.hdfgroup.org/HDF5/ and FileFormats.
- Currently, all supported file types can be converted to a Huygens Resolution Pyramid file if they fit in RAM (+ virtual memory/swap space). For files that do not fit in memory, the list of compatible file types is still limited to: (Huygens) HDF5, ICS/ICS2, OME Tiff, OME, TIFF, Abberior MSR/OBF, Olympus VSI, Zeiss CZI, Leica LIF, LOF, XLIF, Imaris 5.5 HDF5 version. Attempting to convert non-supported files in Huygens will prompt you with a warning and bugreport option. This gives us insight on what formats to include support for in future patches.